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CCDC50 coiled-coil domain containing 50 [ Homo sapiens (human) ]

Gene ID: 152137, updated on 27-Nov-2024

Summary

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Official Symbol
CCDC50provided by HGNC
Official Full Name
coiled-coil domain containing 50provided by HGNC
Primary source
HGNC:HGNC:18111
See related
Ensembl:ENSG00000152492 MIM:611051; AllianceGenome:HGNC:18111
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
YMER; C3orf6; DFNA44
Summary
This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains. Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the protein is expressed in the inner ear during development and postnatal maturation and associates with microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in fat (RPKM 19.1), ovary (RPKM 13.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See CCDC50 in Genome Data Viewer
Location:
3q28
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (191329394..191398659)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (194145445..194207797)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (191047183..191116448)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986171 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:190875631-190876830 Neighboring gene NANOG hESC enhancer GRCh37_chr3:190909180-190909700 Neighboring gene OSTN antisense RNA 1 Neighboring gene osteocrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:191019724-191020249 Neighboring gene urotensin 2B Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:191046750-191047351 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:191047352-191047952 Neighboring gene Sharpr-MPRA regulatory region 6572 Neighboring gene PYDC2 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217087-191217641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217642-191218195 Neighboring gene pyrin domain containing 2 Neighboring gene uncharacterized LOC124909472

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Blagoev B, et al. Nat Biotechnol, 2004 Sep. PMID 15314609
  2. Ymer acts as a multifunctional regulator in nuclear factor-κB and Fas signaling pathways. Tsukiyama T, et al. Mol Med, 2012 May 9. PMID 22331027, Free PMC Article
  3. CCDC50 promotes tumor growth through regulation of lysosome homeostasis. Jia P, et al. EMBO Rep, 2023 Oct 9. PMID 37672005, Free PMC Article
  4. Inhibition of NF-kappaB signaling via tyrosine phosphorylation of Ymer. Kameda H, et al. Biochem Biophys Res Commun, 2009 Jan 23. PMID 19059208
  5. A novel locus for autosomal dominant nonsyndromic hearing loss (DFNA44) maps to chromosome 3q28-29. Modamio-Høybjør S, et al. Hum Genet, 2003 Jan. PMID 12483295

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CCDC50 promotes tumor growth through regulation of lysosome homeostasis.
    Title: CCDC50 promotes tumor growth through regulation of lysosome homeostasis.
  2. Molecular profiling of clinical remission in psoriatic arthritis reveals dysregulation of FOS and CCDC50 genes: a gene expression study.
    Title: Molecular profiling of clinical remission in psoriatic arthritis reveals dysregulation of FOS and CCDC50 genes: a gene expression study.
  3. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
    Title: Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
  4. A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.
    Title: A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.
  5. Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
    Title: Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
  6. Up to now, merely 7 loci have been linked to mid-frequency hearing loss. Only four genetic mid-frequency deafness genes, namely, DFNA10 (EYA4), DFNA8/12 (TECTA), DFNA13 (COL11A2), DFNA44 (CCDC50), have been reported to date. [review]
    Title: Research progress in pathogenic genes of hereditary non-syndromic mid-frequency deafness.
  7. Ymer acts as a regulator downstream of several receptors and that Ymer functions as a positive or negative regulator in a signaling pathway-dependent manner.
    Title: Ymer acts as a multifunctional regulator in nuclear factor-κB and Fas signaling pathways.
  8. CCDC50 is required for survival in mantle cell lymphoma and chronic lymphocytic leukemia cells and controls NFkappaB signaling
    Title: Gene knockdown studies revealed CCDC50 as a candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia.
  9. These findings demonstrate that Ymer is likely to be a negative regulator for the NF-kappaB signaling pathway.
    Title: Inhibition of NF-kappaB signaling via tyrosine phosphorylation of Ymer.
  10. Ymer functions as a novel inhibitor for the down-regulation of the EGF receptor and plays a crucial role for regulating the amount of the EGF receptor on the cell surface membrane
    Title: Suppression of the ligand-mediated down-regulation of epidermal growth factor receptor by Ymer, a novel tyrosine-phosphorylated and ubiquitinated protein.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal dominant nonsyndromic hearing loss 44
MedGen: C1843895 OMIM: 607453 GeneReviews: Genetic Hearing Loss Overview
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EBI GWAS Catalog

Description
GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
coiled-coil domain-containing protein 50
Names
protein Ymer

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008994.1 RefSeqGene

    Range
    5310..74575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1382

mRNA and Protein(s)

  1. NM_174908.4 → NP_777568.1  coiled-coil domain-containing protein 50 short isoform

    See identical proteins and their annotated locations for NP_777568.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the coding region, compared to variant 2, and encodes the short isoform.
    Source sequence(s)
    AC073365, AJ416916
    Consensus CDS
    CCDS33913.1
    UniProtKB/Swiss-Prot
    Q86VH7, Q8IVM0
    Related
    ENSP00000376250.4, ENST00000392456.4
    Conserved Domains (2) summary
    pfam15295
    Location:7 → 126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus
    cl25732
    Location:63 → 233
    SMC_N; RecF/RecN/SMC N terminal domain

  2. NM_178335.3 → NP_848018.1  coiled-coil domain-containing protein 50 long isoform

    See identical proteins and their annotated locations for NP_848018.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longer transcript and encodes the long isoform.
    Source sequence(s)
    AC073365, AJ557013
    Consensus CDS
    CCDS33912.1
    UniProtKB/Swiss-Prot
    Q8IVM0
    Related
    ENSP00000376249.4, ENST00000392455.9
    Conserved Domains (1) summary
    pfam15295
    Location:7 → 126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    191329394..191398659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512460.2 → XP_011510762.1  coiled-coil domain-containing protein 50 isoform X1

    Conserved Domains (1) summary
    pfam15295
    Location:7 → 126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    194145445..194207797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345382.1 → XP_054201357.1  coiled-coil domain-containing protein 50 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IVM0.1 GenPept UniProtKB/Swiss-Prot:Q8IVM0

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